\HeaderA{plotNormalizedData}{plot estimated absolute levels of two conditions}{plotNormalizedData}
\keyword{hplot}{plotNormalizedData}
\begin{Description}\relax
plot estimated absolute levels of any two user-specified conditions. The values in the plot
are in log scale.
\end{Description}
\begin{Usage}
\begin{verbatim}
plotNormalizedData(data, condition = c(1, 2), xlab = NULL, ylab = NULL,
                   main = NULL,xlim = NULL, ylim = NULL, pch = 19,
                   cex = 0.2,col = "black", diag=TRUE, diagcol="blue",
                   diaglwd=1.5, ...)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{data}] matrix containing estimated absolute levels. columns are conditons and
rows are genes.
\item[\code{condition}] integer vector giving the two conditions to be plotted.
\item[\code{xlab}] a title for the x axis.
\item[\code{ylab}] a title for the y axis.
\item[\code{main}] an overall title for the plot. 
\item[\code{xlim}] the x limits (min,max) of the plot.
\item[\code{ylim}] the y limits of the plot.
\item[\code{pch}] an integer code for one of a set of plotting characters 
or symbols for the spike data set. Default is 19.
\item[\code{cex}] a numerical value giving the amount by which points
should be scaled relative to the default. Default is 0.2.
\item[\code{col}] the color of the points. Default is black.
\item[\code{diag}] a logical value. Add diagonal on the plot if it is \code{TRUE}. 
Default is \code{TRUE}.
\item[\code{diagcol}] the color of the diagonal. Default is blue.
\item[\code{diaglwd}] the width of the diagonal. Default is 1.5.
\item[\code{...}] other graphical parameters can be used in function
\code{\LinkA{plot}{plot}}. 
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
The function polts estimated absolute expression levels of two conditions. It accepts
expression levels from the argument 'data', which should have the same data format as 
the output value of the function \code{\LinkA{NormalizeData}{NormalizeData}}.

The two conditions to be plotted should be specified by the argument \code{condition}. 
The \code{condition} should be a numeric vector with length two and it should be subset
of condition vector of the design matrix. see function \code{NormalizeData}.

see other graphic functions for the other arguments.
\end{Details}
\begin{Value}
A plot is created on the current graphics device.
\end{Value}
\begin{Author}\relax
Hui Zhao
\end{Author}
\begin{Examples}
\begin{ExampleCode}
# load data: normalized data
data(normdata)
        
# specify the two conditions to be plotted.
cond <- c(1,2)
        
# use the default values for other parameters.
plotNormalizedData(normdata,condition = cond)
\end{ExampleCode}
\end{Examples}

